Koran desecration

... death is the penalty for desecrating a Koran in Saudi Arabia, Iran, Afghanistan, and elsewhere. Egypt is milder, there one would be sentenced to several years in prison under Article 161 of the penal code for “publicly insulting Islam,” or perhaps Article 98, “inciting sectarian strife”; similar patterns are followed in more moderate Muslim countries. [1]

Guantanamo incident

In 2005, there were "reports that a Koran was desecrated at the US detention centre at Guantanamo",[1]
which led to expressions of official protest as well as deadly anti-US protests, although it turned out the worst offenders were the prisoners themselves.

Media scrutiny focused on allegations that US personnel had stepped on, thrown, or dampened the Koran. An unconfirmed report in Newsweek sparked deadly riots in at least one Islamic country.

"The Afghan interior ministry says four people were killed, and more than 70 injured."[2]

However, Brig. Gen. Jay Hood, the commander of the detention center, found:

... 15 cases of detainees mishandling their own Korans. "These included using a Koran as a pillow, ripping pages out of the Koran, attempting to flush a Koran down the toilet and urinating on the Koran." In the most recent of those 15 cases, a detainee on Feb. 18 allegedly ripped up his Koran and handed it to a guard, stating that he had given up on being a Muslim. Several guards witnessed this, Hood reported.[3]